Team:Newcastle/Meetings/30 March 2009

From 2009.igem.org


Contents

30/03/2009 - iGEM Meeting

  • 14:00 start CLT601
  • Team members absent: Craig, Arun

Action points from the last meeting

  • Develop software systems which stimulates the system (Ongoing)
    • 10% sporulate or 10% continue as vegetative cells - Modelling
  • Familiarise self with BioBricks - ALL
    • List all the BioBricks needed (Current job)
    • Create big flowchart (with gene names) (Current job)
    • Organise a Biobrick tutorial with Anil for a week on Thursday?
  • Use software such as X-Mind for collaborative ideas (Ongoing)
  • Look up safety regulations (Ongoing - Advisors)

Agenda of the Meeting

  • Post paragraph, and maybe wiki-design on main wiki (DONE, No formatting)
  • Create a Flowchart (big with genes) (Done on whiteboard, to create electronically)

Minutes

  • Hand out work for preparation before meeting on Wednesday (11:00am CLT.601)
    • Arun - DNA rearrangement + germination gene regulation
    • Jess – SmtA BB + triggering
    • James – CadA system biobrick
    • Matt – Czr+ArsR+BS
    • Goksel – SinI, SinR SS
    • Hanny – Mnth BB (+Sporulation?)
    • Jane – Triggering Spoulation
  • Looked at other teams wikis (Not many with ideas up)
  • Formal meeting on Thursday 4pm

Meeting 02/04/2009

Agenda of the meeting

  • Show our flowchart/presentation
  • Run through individual research/biobricks

Media:Flowchart_and_BioBricks_for_Bacillus_subtilis.ppt‎


Minutes of the meeting

  • Members present - James, Matt, Jess, Hanny, Goksel
  • Advisors present - Morgan, Matt
  • Bacillus subtilis should always be written as italic. Gene names should start with lowercase whereas protein name should start with uppercase.
  • Do not use green and red colous on presentations.
  • When a protein sequence is known, to find similar proteins do a blast search.
  • To control cadA system directly by ArsR and CzrR, we can insert the binding sites of these proteins into the binding site of CadA.
  • Cd uptake in bacteria is preferred to other metals like Zinc.

Action Points

  • Watch out for other team's wikis. Every week give a review for 5 minutes for other wikis
  • Combine the first two boxes on the presentation.
  • The diagram shouls also include the system that pumps out Cd
  • The first stochastic switch should be wired to Cd sensing system directly whereas the second one should be influenced by the system.
  • We should also model the state when there is no metal
  • Always use DNa rearrangement upon Cd exposure.
  • While doing a presentation, create a table and display which genes are ON and OFF for each step
  • Model Cd uptake using a CellML model
  • Display the spore timeline while presenting the required actions step by step
  • Do not use GFP inside biobricks. In this way they are not modular.
  • List the names of genes that need to be knocked out. E.g mntH.
  • For each gene, specify whether the gene exits in B. subtilis or it is taken from another organism.
  • Investigate if arsR has another name in literature.
  • Investigate the operator site of arsR
  • Investigate how cadA is regulated. We can use sigma factors to regulate cadA system or we can expres a repressor to deactivate the system.
  • Model the following sub systems
    • Cd pumps. we can then decide how many of them we need
    • AND gate for metal sensing
    • Stochastic swicthes
    • DNA rearrangement
    • Population of cells
    • Smta - sponge system
    • Number of metals that a spore can store



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